A major project which involves the TIS is the definition of molecular biomarkers for autoimmune and autoinflammatory diseases. In collaboration NHGRI investigators we have shown that susceptibility to Behcet's disease is associated with genes that regulate the immune response. We observed that monocytes of normal individuals carrying the protective allele express lower levels of IL-23R, and we are now investigating a correlation with the different monocyte populations. We have also investigated the role of cytokines secreted by cells from patients with mutations in ADA2 and shown that upon TLR ligand stimulation ADA2 patients cells secreted increased levels of IL-10, TRAIL and CXCL1. Similarly, circulating (serum) levels of IL-10 and CxCL10 were found to be increased in ADA2 patients. A manuscript reporting these findings is currently under revision. We are also continuing our collaboration with NHGRI investigators assessing the cytokine-secreting capabilities of patients with Erdheim-Chester Disease (ECD), a rare, non-familial multisystem disorder characterized by proliferation and infiltration of non-Langerhans histocytes into multiple organs. Previous reports on the role of cytokines in ECD are few and variable; we are comparing the cytokine secretion levels of ECD patients with normal controls after stimulation of PBMCs. These assays will allow us to better understand the mechanisms of inflammatory processes underlying these diseases and may lead to potential novel therapeutic approaches. As mentioned above, the discovery of protein patterns as biomarkers of disease or therapeutic efficacy is a major objective of the TIS. We have been investigating novel approaches for the treatment of autoimmune diseases and are currently involved in collaboration with the O'Shea group and Pfizer (via a CRADA). We aim to define the mechanism of action of Jak inhibitors like tofacitinib in immune cells. We found that tofacitinib reprograms the cell metabolism status from aerobic glycolysis to oxidative phosphorylation. These data suggest that one aspect of the immune-modulatory actions of tofacitinib may be related to its effect on metabolism. Ultimately, this can be used as a biomarker in tofacitinib-treated patients in clinical studoes. Moreover, we investigated an effect of tofacitinib in CD8+ T cells by analyzing an animal model of CD8+ T cell-mediated graft-versus-host like disease. Tofacitinib decreased CD8+ T cell proliferation and activation. Also, tofacitinib directly inhibits IFN-gamma-induced keratinocyte activation. The TIS has also continued the project generating inducible pluripotent stem cells (iPS). We have generated iPS cells from a patient with HLA B-27+ Ankilosing Spondilitys and one patient with CANDLE as well as one normal control. We have demonstrated their pluripotency by assessing specific markers and embryoid body formation capacity. Furthermore, iPSCs were differentiated into cardiomyocytes that spontaneously began beating. Our research will now focuson showing that such cells are a powerful new tool for studying the pathogenesis of human diseases for pharmacological and toxicological testing as well as cell-based therapy. The TIS is also providing support to several projects carried out at NIAMS to improve the understanding of the genetic determinants of autoimmune, autoinflammatory and musculoskeletal diseases using the Illumina HiSeq 2000 and the MiSeq for ultra high-throughput DNA sequencing. With Dr. Sartorellis group, Aster Juan continues studies to understand how Notch affect Ezh2 methyl transferase activity in skeletal muscle and ES cells by examining histone modifications as well as gene expression changes and assessing the occupancies of Ago2 in the genome in order to discover the novel mechanism of nuclear Ago2 function using ChIP-Seq and RNA-Seq. Stefania DellOrso studies the contribution of the NAD+-dependent histone deacetylase SirT1 in Satellite Cells (Scs) biology. We are currently analyzing SCs from WT and Pax7-Cre:SIRT1fl/fl mice by RNA-seq as well as Sirt1 and H4K16ac genomic occupancy byChIP-seq. Xuesong Feng studies the function of Ezh2 in regulating embryonic cerebellum development to dissect the role of Ezh2 on the cerebellar global gene expression changes and its significance on neurogenesis. With Dr. Yuka Kanno we are analyzing genomic organization of T lymphocytes to understand the gene regulatory mechanism for T helper cell fate specification. We have extensively performed transcriptome mapping by RNA-Seq to understand phenotypic difference among T helper subsets. We have extended our catalogue of transcription factor mapping to include the transcriptional repressor Bach2. We found that Bach2 is a key regulator of immune homeostasis. We have also explored the role of type I IFN in regulating T helper subset called follicular helper T cells. With Dr. Rafael Casellas and Kyong-Rim Kieffer we are trying to map the promoter-enhancer landscape in differentiated B-cells and pluripotent ES cells to study the ontogeny and dynamics of regulatory elements in the genome and their influences on gene expression. Laura Vian is studying the physiological roles of CTCF factors. By generating stable Knock-in mutants for several of these zinc finger and using ChIP-Seq and RNA-Seq we are analyzing how these mutants affect the DNA-CTCF binding and how this could alter the cell transcriptome. Dr. Rosa Munoz Cano in the Rivera lab continues the evaluation and comparison of four clinical anaphylaxis phenotypes using RNA-Sequencing. With Dr. Morassos lab, Elisabetta Palazzo uses RNAseq and ChIPseq methodologies to define Dlx3 function and its targets in skin cells and understanding its molecular function. Olivier Duverger investigates the function of Dlx3 in enamel formation and uses RNA-Seq to characterize the transcriptome of enamel organs in which Dlx3 was deleted using a conditional knockout approach, and identify genes and pathways controlled by Dlx3 during enamel production and maturation. With Drs. Leon Nesti and Youngmi Ji we have performed RNA-Seq studies elucidating how activation via injury affects the mesenchymal progenitor cells and whether trauma may contribute to pathological differentiation of these cells and formation of heterotopic ossification. Outside NIAMS IRP we continue collaborations with Dr. Melodie Weller from NIDCR sequencing a novel RNA viral isolate identified in human serum and resequencing an amplicon which carries a mutation present in a population of autoimmune patients initially identified through comparative genomic hybridization (CGH) analysis. With Dr. Nussenzweigs group (NCI), Jacqueline Barlow is mapping replication-induced DNA damage stress in response to the drug hydroxyurea and the recruitment of DNA repair proteins to AID-dependent and in B cells. Aysegul Ergen studies the role of MLL4 in hematopoietic stem cells and MLL1-AF9-induced leukemogenesis in stem/progenitor cells by crossing MLL4 with Mx-Cre mice and then testing MLL4 knock-out bone marrow cells for MLL1-AF9 induced transformation. MLL1-AF9 signature genes were found to be down-regulated in MLL4 deficient cells whereas myeloid maturation genes were up-regulated. We support the clinical research protocol 08-DK-0098 (Dr. Stephen Wank, (NIDDK), Natural History of Familial Carcinoid, with the aim of determining the genetic basis of small intestinal carcinoid tumors that occur in families with an autosomal dominant mode of inheritance. We performed RNA-Seq on tumor samples to assess sequence variation in expressed genes, abnormal variation in exon splicing and variation in the expression of genes along a given pathway that may help understand the process of carcinogenesis in these rare tumors.